Hm, I had a similar(?) case for the lucrative route BRU-ATH. I was waitlisted and there was availability in C (at least 4 seats) at T-72. However, my upgrade did not automatically clear (my booking still showed the 2 bookings), and then C availability became 0. So, naturally, I thought that I did not get the upgrade. Buuuuut, at T-48 when tried to do checkin I was not able to (showed me in C, but could not complete it). Called the call center and they told me that the upgrade was cleared but not taken care off. After 7 minutes on the phone, got the upgrade and managed to checkin. C is full (2 rows).
I asked but did not get answer as to why my upgrade did not automatically clear (and I had to make a call).